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If I want to calibrate on a canvas that is in a different window as the canvas I will be doing all my tracking on, is there any way to set their calibration values as the same value if the canvas sizes are different? I have tried setting the distances as a percentage of the whole but I do not think that works because the pixel amounts would still be different.

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I'm not sure what your application structure is, but is it possible that you could pass in your canvas size values into a method? Our team doesn't use an additional window to set the calibration, but perhaps you could pass in values like canvas.getHeight() and canvas.getWidth()? Or even pass in your entire canvas?